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The Rat Genome Database (RGD): developments towards a phenome database

N. de la Cruz
2004 Nucleic Acids Research  
Here, we report on RGD's development towards creating a phenome database. Recent developments can be categorized into three groups.  ...  The Rat Genome Database (RGD) (http://rgd.mcw. edu) aims to meet the needs of its community by providing genetic and genomic infrastructure while also annotating the strengths of rat research: biochemistry  ...  Here, we report on RGD's development towards creating a phenome database. Recent developments can be categorized into three groups.  ... 
doi:10.1093/nar/gki050 pmid:15608243 pmcid:PMC540004 fatcat:gnzke5nrlfbmnikqraddcnazea

OUP accepted manuscript

2019 Database: The Journal of Biological Databases and Curation  
The Rat Genome Database (RGD) PhenoMiner tool has provided the first step in this effort by standardizing and integrating data from individual studies as well as NBRP and PhysGen. iii Methods Our work  ...  Capturing these phenotypes in a centralized database provides researchers with an easy method for choosing the appropriate strains for their studies.  ...  Based on the success of this project, the Rat Genome Database will develop a Precision Models Portal to present these data and link to others to provide a rich resource for investigators.  ... 
doi:10.1093/database/baz037 fatcat:ifj26ad6grh2vcqvbtnxoevdwq

BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources

Chunlei Wu, Camilo Orozco, Jason Boyer, Marc Leglise, James Goodale, Serge Batalov, Christopher L Hodge, James Haase, Jeff Janes, Jon W Huss, Andrew I Su
2009 Genome Biology  
However, the landscape of these online resources is highly fragmented, and scientists often visit dozens of these sites for each gene in a candidate gene list.  ...  Online gene annotation resources are indispensable for analysis of genomics data.  ...  This work was supported by grant number GM083924 (to AIS) from the National Institute of General Medical Sciences (NIGMS) at the National Institutes of Health, and by the Novartis Research Foundation.  ... 
doi:10.1186/gb-2009-10-11-r130 pmid:19919682 pmcid:PMC3091323 fatcat:gfkh6qc5sra3lcf7tm73a7xwym

Phenotype Data: A Neglected Resource in Biomedical Research?

Philip Groth, Bertram Weiss
2006 Current Bioinformatics  
Despite the importance of how specific genetic alterations contribute to the development of diseases, surprisingly little effort has been made towards exploiting systematically the current knowledge of  ...  In the past, genes were characterized with the help of so-called "forward genetics" studies in model organisms, relating a given phenotype to a genetic modification.  ...  ACKNOWLEDGEMENTS We are grateful to Bernard Haendler (Schering AG) for useful discussions of the manuscript and to the referee's valuable comments and suggestions.  ... 
doi:10.2174/157489306777828008 fatcat:kkgtcwoluzc7xlt7uwpp5k7zyu

Inter-database annotation linkages in model organism databases

W. John MacMullen
2006 Proceedings of the American Society for Information Science and Technology  
Research goals This project is a component of the larger Annotation of Structured Data project described in MacMullen (2005).  ...  While all databases had the potential to be linked to all others via GO, only some databases had non-GO links to others.  ...  The Rat Genome Database (RGD): Developments towards a phenome database. Nucleic Acids Research 33(1), D485-D491.  ... 
doi:10.1002/meet.14504201268 fatcat:yk6e22ejfvbplganhd3bmehwz4

Integrating Evolutionary Genetics to Medical Genomics: Evolutionary Approaches to Investigate Disease-Causing Variants [chapter]

Ugur Sezerman, Tugce Bozkurt, Fatma Sadife Isleyen
2020 Molecular Medicine [Working Title]  
Finally, we present an example of a real-life case where the use of evolutionary genetics information facilitated the discovery of disease-causing variants in medical genomics.  ...  However, identifying the potential effects of the variations and their association with a particular disease phenotype is the main challenge in this field.  ...  Rat Genome Database (RGD) RGD provides genetic, genomic, phenotypic, and disease-related data for the laboratory rat, Rattus norvegicus.  ... 
doi:10.5772/intechopen.92738 fatcat:gy7xau3ulvcvvg3uvhvg6yc2we

Establishment and application of information resource of mutant mice in RIKEN BioResource Research Center

Hiroshi Masuya, Daiki Usuda, Hatsumi Nakata, Naomi Yuhara, Keiko Kurihara, Yuri Namiki, Shigeru Iwase, Toyoyuki Takada, Nobuhiko Tanaka, Kenta Suzuki, Yuki Yamagata, Norio Kobayashi (+2 others)
2021 Laboratory Animal Research  
The BioResource Research Center also released a genomic variation database of mouse strains established in Japan and Western Europe, MoG+ (https://molossinus.brc.riken.jp/mogplus/), and a database for  ...  The number and types of mouse resources have been rapidly growing due to the development of genetic modification technology with associated information of genomic sequence and phenotypes.  ...  Kawashima S. in Database Center for Life Science and Dr. Kawamoto S. in National Institute of Genetics for discussion on data integration and standardization of bioresource data.  ... 
doi:10.1186/s42826-020-00068-8 pmid:33455583 fatcat:q2n7degp7fhorh3pbljrbshwcu

The RIKEN integrated database of mammals

H. Masuya, Y. Makita, N. Kobayashi, K. Nishikata, Y. Yoshida, Y. Mochizuki, K. Doi, T. Takatsuki, K. Waki, N. Tanaka, M. Ishii, A. Matsushima (+16 others)
2010 Nucleic Acids Research  
Through the development of this database, we propose a novel methodology for the development of standardized comprehensive management of heterogeneous data sets in multiple databases to improve the sustainability  ...  The database integrates not only RIKEN's original databases, such as FANTOM, the ENU mutagenesis program, the RIKEN Cerebellar Development Transcriptome Database and the Bioresource Database, but also  ...  ACKNOWLEDGEMENTS The authors thank Drs Kaoru Saijyo, Kazuyuki Mekada and Hatsumi Nakata in RIKEN BRC to help data import from Resource database to SciNetS.  ... 
doi:10.1093/nar/gkq1078 pmid:21076152 pmcid:PMC3013680 fatcat:72k5lclp2vbade5eklbvfrpzxi

BN phenome: detailed characterization of the cardiovascular, renal, and pulmonary systems of the sequenced rat

Anne E. Kwitek, Howard J. Jacob, John E. Baker, Melinda R. Dwinell, Hubert V. Forster, Andrew S. Greene, Mary Pat Kunert, Julian H. Lombard, David L. Mattson, Kirkwood A. Pritchard, Richard J. Roman, Peter J. Tonellato (+1 others)
2006 Physiological Genomics  
The postgenome era has provided resources to link disease phenotypes to the genomic sequence, i.e., creating a disease "phenome."  ...  Editor-in-Chief, Physiological Genomics. BN phenome: detailed characterization of the cardiovascular, renal, and pulmonary systems of the sequenced rat.  ...  Roman are co-founders and board members of PhysioGenix, Incorporated, which has a commercial license for the consomic rat strains.  ... 
doi:10.1152/physiolgenomics.00288.2005 pmid:16478827 fatcat:5lei55cvl5ea3pab7xtv5ci7me

A meta-analysis of QTL for diabetes-related traits in rodents

Christian Schmidt, Nina P. Gonzaludo, Sarah Strunk, Stefan Dahm, Johannes Schuchhardt, Frank Kleinjung, Stefan Wuschke, Hans-Georg Joost, Hadi Al-Hasani
2008 Physiological Genomics  
The analysis revealed significant evidence for linkage of glucose levels, insulin levels, and glucose tolerance to 27 different segments of the mouse genome.  ...  The most prominent consensus regions [localized to chromosomes 2, 4, 7, 9, 11, 13, and 19; logarithm of odds (LOD) scores 10.5-17.4] cover ϳ11% of the mouse genome and collectively contain the peak markers  ...  David Adler for providing the idiograms of the mouse chromosomes.  ... 
doi:10.1152/physiolgenomics.00267.2007 pmid:18397992 fatcat:g4wu6wyrmrcmpps5eiqrhf36ci

SNP and haplotype mapping for genetic analysis in the rat

Kathrin Saar, Alfred Beck, Marie-Thérèse Bihoreau, Ewan Birney, Denise Brocklebank, Yuan Chen, Edwin Cuppen, Stephanie Demonchy, Joaquin Dopazo, Paul Flicek, Mario Foglio, Asao Fujiyama (+37 others)
2008 Nature Genetics  
To facilitate access to the data in the context of further information, the data represented here has been integrated in other databases, namely the Rat Genome Database (RGD; see URL 1) and GeneNetworks  ...  To study genome-wide genetic variation, we initiated the genetic dissection of the ancestral segments making up the most commonly used rat inbred lines, and we developed a comprehensive open resource of  ... 
doi:10.1038/ng.124 pmid:18443594 pmcid:PMC5915293 fatcat:nibx2hhnirc4hmi7ijnbwuvmtm

The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species

2019 Nucleic Acids Research  
The Monarch Initiative (https://monarchinitiative.org) integrates information on genes, variants, genotypes, phenotypes and diseases in a variety of species, and allows powerful ontology-based search.  ...  redesigned website); and community development.  ...  ACKNOWLEDGEMENTS We would like to thank the many people who have contributed to the improvements and updates we have reported here, including (but not limited to) Donna Maglott, Anne Pariser and Janine  ... 
doi:10.1093/nar/gkz997 pmid:31701156 pmcid:PMC7056945 fatcat:tramusfgz5eufn2aguuzzasafi

Selection of extreme phenotypes: the role of clinical observation in translational research

José Luis Pérez-Gracia, Alfonso Gúrpide, María Gloria Ruiz-Ilundain, Carlos Alfaro Alegría, Ramon Colomer, Jesús García-Foncillas, Ignacio Melero Bermejo
2010 Clinical and Translational Oncology  
Although some databases for animal species are being developed, progress in humans is slow, probably due to the multifactorial origin of many human diseases and to the intricacy of accurately classifying  ...  The consistent results achieved suggest that it seems logical to further develop this strategy as a methodology to study human disease, including cancer.  ...  Nucleic Acids Res 37:D720-730 6. de la Cruz N, Bromberg S, Pasko D et al (2005) The Rat Genome Database (RGD): developments towards a phenome database. Nucleic Acids Res 33:D485-491 7.  ... 
doi:10.1007/s12094-010-0487-7 pmid:20231122 pmcid:PMC2997959 fatcat:mp4dh3aysjc5popt45es63x7w4

An Integrative Genomic Approach to Uncover Molecular Mechanisms of Prokaryotic Traits

Yang Liu, Jianrong Li, Lee Sam, Chern-Sing Goh, Mark Gerstein, Yves A. Lussier
2006 PLoS Computational Biology  
Here, we developed a high throughput computational approach, and demonstrated for the first time the feasibility of integrating large quantities of prokaryotic phenotypes along with genomic datasets for  ...  With mounting availability of genomic and phenotypic databases, data integration and mining become increasingly challenging.  ...  We acknowledge the support of the following grants: US National Institutes of Health (NIH)/National Library of Medicine 1K22 LM008308 (Semantic Approaches to Phenotypic Database Analysis), and NIH/National  ... 
doi:10.1371/journal.pcbi.0020159 pmid:17112314 pmcid:PMC1636675 fatcat:whsrbwaxx5gvhbl4ebm3rolwum

An integrative genomic approach to uncover molecular mechanisms of prokaryotic traits

Yang Liu, Jianrong Li, Lee Sam, Chern-Sing Goh, Mark B Gerstein, Yves Lussier
2005 PLoS Computational Biology  
Here, we developed a high throughput computational approach, and demonstrated for the first time the feasibility of integrating large quantities of prokaryotic phenotypes along with genomic datasets for  ...  With mounting availability of genomic and phenotypic databases, data integration and mining become increasingly challenging.  ...  We acknowledge the support of the following grants: US National Institutes of Health (NIH)/National Library of Medicine 1K22 LM008308 (Semantic Approaches to Phenotypic Database Analysis), and NIH/National  ... 
doi:10.1371/journal.pcbi.0020159.eor fatcat:5djmteddz5dstkqoibvggwdn7q
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